Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Area of Science:

• Environmental microbiology
• Virology
• Public health surveillance

Background:

• Early detection of SARS-CoV-2 variants is crucial for effective public health interventions.
• Clinical testing for lineage prevalence is often infeasible at scale and can be biased.
• Wastewater surveillance offers a less biased method for tracking regional infection dynamics.

Purpose of the Study:

• To develop and deploy improved wastewater genomic surveillance methods for early SARS-CoV-2 variant detection.
• To overcome limitations of low-quality sequence data and relative lineage abundance estimation in wastewater.
• To compare wastewater-based genomic surveillance with clinical sequencing over a 295-day period.

Main Methods:

• Developed enhanced virus concentration protocols for wastewater samples.
• Deployed deconvolution software to resolve multiple virus strains from mixed wastewater samples.
• Conducted a 295-day concurrent wastewater and clinical sequencing effort on a university campus and surrounding county.

Main Results:

• Emerging SARS-CoV-2 variants of concern were detected up to 14 days earlier in wastewater.
• Identified instances of virus spread not captured by clinical genomic surveillance.
• Demonstrated the ability to resolve multiple virus strains from wastewater with improved accuracy.

Conclusions:

• Wastewater genomic surveillance provides a scalable solution for early SARS-CoV-2 variant detection.
• This approach enhances community prevalence estimates and identifies cryptic transmission.
• Improved wastewater surveillance can significantly aid public health response to evolving viral threats.